SOAPy_st.tl.cal_spatialDE

SOAPy_st.tl.cal_spatialDE(adata: AnnData, gene_name: list | str | None = None, spatial_in_obsm: str = 'spatial') → DataFrame

Calculate SpatialDE analysis on spatial omics data. Doi: 10.1038/nmeth.4636 Github: https://github.com/Teichlab/SpatialDE

Parameters

adataanndata.AnnData

An AnnData object containing spatial omics data and spatial information.

gene_nameUnion[list, str, None], optional

List of genes of interest or a single gene name to focus the analysis on. If None, the analysis will consider all genes in the dataset.

spatial_in_obsmstr

The key of spatial coordinates in adata.obsm

Returns

pd.DataFrame

A Pandas DataFrame containing the results of the SpatialDE analysis.